Variant report

Variant	rs12599564
Chromosome Location	chr16:81348396-81348397
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr16:81348271-81348672	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr16:81348217-81348931	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:81347960-81348940	PFSK-1	brain:	n/a	n/a
4	MAFK	chr16:81348360-81348580	HepG2	liver:	n/a	n/a
5	SP1	chr16:81348151-81348743	GM12878	blood:	n/a	chr16:81348481-81348492 chr16:81348442-81348463 chr16:81348478-81348492
6	SP1	chr16:81348193-81348646	GM12878	blood:	n/a	chr16:81348481-81348492 chr16:81348442-81348463 chr16:81348478-81348492
7	USF1	chr16:81348222-81348591	A549	lung:	n/a	n/a
8	ETS1	chr16:81348107-81348777	A549	lung:	n/a	n/a
9	ELF1	chr16:81348174-81349531	GM12878	blood:	n/a	n/a
10	HNF4G	chr16:81348232-81348737	HepG2	liver:	n/a	n/a
11	RFX5	chr16:81348185-81348616	GM12878	blood:	n/a	chr16:81348452-81348461
12	GABPA	chr16:81348155-81348707	SK-N-SH	brain:	n/a	chr16:81348546-81348560 chr16:81348431-81348440
13	NFYB	chr16:81348191-81348620	Hela-S3	cervix:	n/a	chr16:81348450-81348464 chr16:81348449-81348464 chr16:81348449-81348464 chr16:81348452-81348462 chr16:81348451-81348466 chr16:81348451-81348464
14	CREB1	chr16:81348094-81349077	GM12878	blood:	n/a	n/a
15	POLR2A	chr16:81348209-81348760	HUVEC	blood vessel:	n/a	n/a
16	PML	chr16:81348019-81348881	MCF-7	breast:	n/a	n/a
17	UBTF	chr16:81348168-81348847	K562	blood:	n/a	n/a
18	SIN3AK20	chr16:81348158-81348930	K562	blood:	n/a	n/a
19	GTF2B	chr16:81348216-81348597	K562	blood:	n/a	n/a
20	FOS	chr16:81348346-81348543	MCF10A-Er-Src	breast:	n/a	chr16:81348451-81348460
21	CREB1	chr16:81348007-81349147	K562	blood:	n/a	n/a
22	MAZ	chr16:81348137-81349555	K562	blood:	n/a	n/a
23	SIX5	chr16:81348366-81348661	K562	blood:	n/a	n/a
24	POLR2A	chr16:81348310-81348659	K562	blood:	n/a	n/a
25	NFE2	chr16:81348336-81348525	GM12878	blood:	n/a	n/a
26	MYC	chr16:81348147-81348884	K562	blood:	n/a	n/a
27	ZBTB33	chr16:81348209-81348631	A549	lung:	n/a	n/a
28	PAX5	chr16:81348243-81348610	GM12878	blood:	n/a	n/a
29	CREB1	chr16:81348121-81349043	A549	lung:	n/a	n/a
30	BCLAF1	chr16:81348174-81348754	GM12878	blood:	n/a	chr16:81348469-81348478
31	POLR2A	chr16:81348038-81348807	PFSK-1	brain:	n/a	n/a
32	MYBL2	chr16:81348147-81348767	HepG2	liver:	n/a	n/a
33	MYBL2	chr16:81347296-81348886	HepG2	liver:	n/a	n/a
34	EGR1	chr16:81348218-81348670	GM12878	blood:	n/a	chr16:81348498-81348511 chr16:81348500-81348510 chr16:81348498-81348511 chr16:81348501-81348510 chr16:81348497-81348512 chr16:81348500-81348510 chr16:81348470-81348484 chr16:81348498-81348511 chr16:81348498-81348512 chr16:81348498-81348511 chr16:81348494-81348516 chr16:81348499-81348510
35	MAFK	chr16:81348172-81348820	Hela-S3	cervix:	n/a	n/a
36	TAF7	chr16:81348073-81348817	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr16:81348204-81348911	K562	blood:	n/a	n/a
38	POLR2A	chr16:81347971-81348915	U87	brain:	n/a	n/a
39	ZNF143	chr16:81348307-81348875	Hela-S3	cervix:	n/a	chr16:81348707-81348717 chr16:81348431-81348441
40	MAX	chr16:81348038-81348832	A549	lung:	n/a	n/a
41	TAF1	chr16:81348109-81348746	PFSK-1	brain:	n/a	n/a
42	MYC	chr16:81348274-81348967	MCF-7	breast:	n/a	n/a
43	NR2F2	chr16:81348015-81348929	MCF-7	breast:	n/a	n/a
44	SRF	chr16:81348252-81348690	H1-hESC	embryonic stem cell:	n/a	n/a
45	BRCA1	chr16:81348245-81348717	HepG2	liver:	n/a	n/a
46	MXI1	chr16:81348160-81348819	Hela-S3	cervix:	n/a	n/a
47	E2F6	chr16:81348168-81348988	K562	blood:	n/a	chr16:81348707-81348717 chr16:81348453-81348462 chr16:81348543-81348550
48	MTA3	chr16:81347878-81348926	GM12878	blood:	n/a	n/a
49	POLR2A	chr16:81348158-81348887	GM12892	blood:	n/a	n/a
50	POLR2A	chr16:81348172-81348852	GM10847	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:81348378-81348428	NT2-D1	testis:	n/a
2	chr16:81348372-81348422	SKMC	muscle:	n/a
3	chr16:81348378-81348428	Jurkat	blood:	n/a
4	chr16:81348372-81348422	ovcar-3	ovarian:	n/a
5	chr16:81348372-81348422	GM12892	blood:	n/a
6	chr16:81348372-81348422	AG09309	skin:	n/a
7	chr16:81348372-81348422	A549	lung:	n/a
8	chr16:81348372-81348422	HIPEpiC	eye:	n/a
9	chr16:81348378-81348428	SK-N-SH	brain:	n/a
10	chr16:81348378-81348428	MCF-7	breast:	n/a
11	chr16:81348378-81348428	IMR90	lung:	fetal
12	chr16:81348378-81348428	NH-A	brain:	n/a
13	chr16:81348372-81348422	HUVEC	blood vessel:	n/a
14	chr16:81348372-81348422	ProgFib	skin:	n/a
15	chr16:81348378-81348428	PANC-1	pancreas:	n/a
16	chr16:81348378-81348428	CMK	blood:	n/a
17	chr16:81348372-81348422	MCF-7	breast:	n/a
18	chr16:81348372-81348422	Jurkat	blood:	n/a
19	chr16:81348378-81348428	HEEpiC	esophagus:	n/a
20	chr16:81348378-81348428	NHDF-neo	bronchial:	n/a
21	chr16:81348372-81348422	RPTEC	kidney:	n/a
22	chr16:81348378-81348428	HIPEpiC	eye:	n/a
23	chr16:81348372-81348422	HEK293	kidney:	embryo
24	chr16:81348378-81348428	Hela-S3	cervix:	n/a
25	chr16:81348378-81348428	HMEC	breast:	n/a
26	chr16:81348372-81348422	HRCEpiC	kidney:	n/a
27	chr16:81348378-81348428	A549	lung:	n/a
28	chr16:81348378-81348428	SKMC	muscle:	n/a
29	chr16:81348372-81348422	SK-N-MC	brain:	n/a
30	chr16:81348372-81348422	IMR90	lung:	fetal
31	chr16:81348372-81348422	GM19239	blood:	n/a
32	chr16:81348372-81348422	PrEC	prostate:	n/a
33	chr16:81348378-81348428	Hepatocyte	liver:	n/a
34	chr16:81348378-81348428	GM12891	blood:	n/a
35	chr16:81348378-81348428	PFSK-1	brain:	n/a
36	chr16:81348378-81348428	AG10803	skin:	n/a
37	chr16:81348372-81348422	SK-N-SH_RA	brain:	n/a
38	chr16:81348378-81348428	AoSMC	blood vessel:	n/a
39	chr16:81348378-81348428	ovcar-3	ovarian:	n/a
40	chr16:81348372-81348422	AG04450	lung:	fetal
41	chr16:81348378-81348428	T-47D	breast:	n/a
42	chr16:81348372-81348422	T-47D	breast:	n/a
43	chr16:81348372-81348422	Caco-2	colon:	n/a
44	chr16:81348378-81348428	HPAEpiC	pulmonary alveolar:	n/a
45	chr16:81348378-81348428	HCM	heart:	n/a
46	chr16:81348378-81348428	HEK293	kidney:	embryo
47	chr16:81348378-81348428	HCF	heart:	n/a
48	chr16:81348378-81348428	HAEpiC	amniotic membrane:	n/a
49	chr16:81348378-81348428	AG04450	lung:	fetal
50	chr16:81348372-81348422	HL-60	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81109518..81111024-chr16:81347327..81349963,2	K562	blood:
2	chr16:81038258..81040784-chr16:81347032..81349945,2	K562	blood:
3	chr16:81348181..81349165-chr7:152132447..152133006,2	Hela-S3	cervix:
4	chr11:62622890..62623673-chr16:81347895..81348866,2	Hela-S3	cervix:
5	chr16:81347539..81350872-chr16:81478035..81482618,4	MCF-7	breast:
6	chr16:81038653..81041025-chr16:81346635..81349129,2	MCF-7	breast:
7	chr16:81347950..81350114-chr16:81397372..81401433,3	MCF-7	breast:
8	chr16:81110316..81112473-chr16:81346981..81348533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260495	TF binding region
GAN	TF binding region
ENSG00000260495	CpG island
GAN	CpG island
ENSG00000168003	Chromatin interaction
ENSG00000055609	Chromatin interaction
ENSG00000153815	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000261609	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166451	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10454708	0.95[ASN][1000 genomes]
rs11150384	0.95[ASN][1000 genomes]
rs11150386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12149852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12597517	0.82[ASN][1000 genomes]
rs12924233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16955221	1.00[MEX][hapmap]
rs16955238	1.00[MEX][hapmap]
rs17189030	1.00[MEX][hapmap]
rs3809632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41484544	1.00[MEX][hapmap]
rs4468614	0.95[ASN][1000 genomes]
rs4522413	0.89[ASN][1000 genomes]
rs4598907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4888135	0.95[ASN][1000 genomes]
rs4888137	0.89[ASN][1000 genomes]
rs4889299	1.00[JPT][hapmap]
rs62047162	0.96[EUR][1000 genomes]
rs6564868	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7184259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7186648	0.95[ASN][1000 genomes]
rs7195134	0.95[ASN][1000 genomes]
rs7196075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7200991	1.00[MEX][hapmap]
rs8055879	0.89[ASN][1000 genomes]
rs8060840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9926795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940292	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
5	nsv522890	chr16:81341363-81348396	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81346600-81349400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr16:81346800-81348600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:81346800-81349400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr16:81346800-81349400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr16:81346800-81349800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr16:81346800-81350200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr16:81347000-81349400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr16:81347000-81349600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:81347000-81349600	Active TSS	NHLF	lung
10	chr16:81347000-81349800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:81347000-81350000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr16:81347000-81350000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr16:81347000-81350200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr16:81347200-81349800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr16:81347200-81350000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr16:81347200-81350400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr16:81347400-81348400	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr16:81347400-81348400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr16:81347400-81348400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr16:81347400-81348400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr16:81347400-81349000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr16:81347400-81349200	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr16:81347400-81349400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr16:81347400-81349600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:81347400-81349800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:81347400-81350000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr16:81347600-81348400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr16:81347600-81349400	Active TSS	Brain Angular Gyrus	brain
29	chr16:81347600-81349600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:81347600-81349600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr16:81347600-81349600	Active TSS	Fetal Kidney	kidney
32	chr16:81347600-81349600	Active TSS	HSMM	muscle
33	chr16:81347600-81349800	Active TSS	A549	lung
34	chr16:81347800-81348400	ZNF genes & repeats	Fetal Brain Male	brain
35	chr16:81347800-81348400	Bivalent/Poised TSS	HepG2	liver
36	chr16:81347800-81348800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr16:81347800-81349400	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr16:81347800-81349400	Active TSS	Small Intestine	intestine
39	chr16:81347800-81349400	Active TSS	GM12878-XiMat	blood
40	chr16:81347800-81349600	Active TSS	Brain Cingulate Gyrus	brain
41	chr16:81347800-81349600	Active TSS	Fetal Intestine Small	intestine
42	chr16:81347800-81349600	Active TSS	Gastric	stomach
43	chr16:81347800-81349600	Active TSS	Stomach Mucosa	stomach
44	chr16:81347800-81349600	Active TSS	Spleen	Spleen
45	chr16:81347800-81349600	Active TSS	NHDF-Ad	bronchial
46	chr16:81347800-81349800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr16:81347800-81349800	Active TSS	Fetal Muscle Trunk	muscle
48	chr16:81347800-81349800	Active TSS	Ovary	ovary
49	chr16:81347800-81349800	Active TSS	Placenta Amnion	Placenta Amnion
50	chr16:81347800-81350200	Active TSS	Right Atrium	heart

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